Since the advent of the polymerase chain reaction (PCR) it has been recognized that nucleic acid amplification methodologies can be used to estimate the initial concentration of a template nucleic acid, providing what is known as quantitative PCR. However, variations in the efficiency or other aspects of an amplification can and do result from a number of different influences on the reactions. Multiplex quantitative PCR, while providing benefits in determining concentrations of multiple nucleic acid sequences in a mixture, presents additional challenges, such as the need for multiple, unique probe sets having different detectable labels.